summarize.features: Summarize features

In zellerlab/siamcat: Statistical Inference of Associations between Microbial Communities And host phenoTypes

Summarize features

Description

This function summarize features on a specific taxonomic level

Usage

summarize.features(siamcat, level = 'g__', 
feature.type='original', verbose=1)

Arguments

siamcat	object of class siamcat-class
level	string, at which level to summarize (e.g. g__ = genus)
feature.type	string, on which type of features should the function work? Can be either "original", "filtered", or "normalized". Please only change this paramter if you know what you are doing!
verbose	integer, control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Details

This function will summarize features at different taxonomic levels, e.g. transform species-level relative abundance into genus-level taxonomic profiles.

The function expects a SIAMCAT object that either contains an entry in the tax_table slot of its phyloseq object, OR a set of feature names which encode taxonomic information, e.g.

k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Acidimicrobiales;..

Then, for a given taxonomic level (e.g. g__), the function will sum up all the relative abundances of features belonging to the same group at that specific taxonomic level.

Please note that this function is currently maturing and not necessarily reliable!!!

Value

object of class siamcat-class with a summarized feature table

Examples

## load the phyloseq example data
data("GlobalPatterns")
## create an example label
label <- create.label(meta=sample_data(GlobalPatterns),
    label = "SampleType",
    case = c("Freshwater", "Freshwater (creek)", "Ocean"))
# run the constructor function
siamcat <- siamcat(phyloseq=GlobalPatterns, label=label, verbose=1)
siamcat <- summarize.features(siamcat, level='Genus', verbose=3)

zellerlab/siamcat documentation built on Feb. 1, 2024, 2:21 a.m.